What dos commands are you trying to run?
I on php 4.3.8 and windows 2000 server found that I can run simple command like help, ping, tracert. I however could not run netstop or netstart commands. I don't believe that it is a php problem rather a windows issue, even from a .bat file saved in the wwwroot the command would just loop, if I then took the same .bat file an moved it out of the wwwroot it worked?
I need to do a sybase prune on an hourly basis so putting a php file out of the wwwroot, that stopped the service then did the sql statements, then started the service. Then I used phpcommand line with the windows task scheduler. If your needs are similar you can reffer to this thread:
http://www.phpbuilder.com/board/showthread.php?s=&threadid=10288993
Good Luck!
Chris